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Brain* is a Software Framework designed to host, manage, visualize and mine large collection of confocal microscopy images. Brain* is currently online with three data collections hosting atlases of the drosophila larva (http://www.larvalbrain.org), adult drosophila (http://fruitfly.tefor.net and https://implegacy.brainbase.at) and zebrafish (http://zebrafish.tefor.net). BrainBaseWeb and BrainGazer are the two available user interfaces to BrainBase data bases providing customized tools to access, visualize, explore and mine the data.
A Historical Note: The framework has been originally developed in context of VT and enhancer trap Gal4 lines of adult drosophila generated by Barry Dickson and his group over several years at the Institute of Molecular Pathology Vienna. The public part of the VT Line Instance of BrainBase provides access to 12 000 images and around 120 identified neurons annotated on a subset of these images. The internal part managed the whole lab image collection during the acquisition process providing instant access spatial image content even in a dynamically growing collection of up to 55.000 3D images.
The original database http://brainbase.imp.ac.at has been taken offline by IMP in June 2018. We are hosting the public VT line collection now at VRVis, accessible via https://implegacy.brainbase.at. BrainGazer is also working for the VT line collection with the new installation - just change the BrainBase settings in BrainGazer to the new address.
Advanced Queries for lines and neurons of interest
Neuron base Search: Query for images/lines expressing a neuron of interest.
Image Based Search: Query for images/lines showing a structure of interest present in a certain query image.
Anatomical Search: Query for lines and neurons with specific staining profiles
Detection and exploration of co-expressions and potential connectivity
Query for arborizations and images showing innervations in certain neuropils or user defined regions.
Overlap computations: Quantify overlaps of staining of a set of lines or annotated arborizations of a set of neurons in arbitrary regions.
neuroMap: Fast hypothesis building on potential connectivity of known neurons.
Classification and comparison
Classify unknown neurons or find similar known neurons.
Cluster images and neurons based on global or local similarity.